From:
`Sent:
`To:
`Subject:
`
`kael.fischer@gmail.com on behalf of Kael Fischer [kael@derisilab.ucsf.edu]
`Monday, May 26, 2008 2:52PM
`Christina Fan
`Re: GERALD run completed in 08051 O_HWI-EAS1 00_0004_FC20f5baaxx/Data/C1-25
`_Firecrest1.8.28_20-05-2008_kaei!Bustard1.8.28_20-05-2008_kaei/GERALD_20-05-2008
`_kael
`
`Good guess on the match codes. the number in the code it the number of apparent snps. The
`numbers are positions in the reference, and optionally a snp position.
`
`see: http://meebo2.ucsf.edu/Solexa/docs/Whole%20genome%20alignments%20using%20ELAND.html
`
`for more detail
`
`On Mon, May 26, 2008 at 2:10 PM, Christina Fan <chfan@stanford.edu> wrote:
`> hi kael,
`> i am guessing that U stands for unique, NM stands for no match and R
`> stands for repeat. But what is the difference between UO and U1 etc.?
`> And what do the 3 numerical entries in field 4, 5, 6 correspond to?
`> thanks!!!
`> christina
`>
`>
`> On May 26, 2008, at 1:46 PM, Kael Fischer wrote:
`>
`>> I wouldn't count on the transfer big files working.
`>>
`>> use gzip -t after your transfer to test the files.
`>>
`>> kael
`>>
`>> On Mon, May 26, 2008 at 1:03 PM, Christina Fan <chfan@stanford.edu> wrote:
`>>>
`>>> hi kael,
`>>> i managed to download lane1 file with my browser.
`>>> if it's too much of a trouble to do the transferbigfiles i can
`>>>download the file one by one with my browser .. doesn't take too
`>>> long ..
`>>> thanks a lot for your help!
`>>> christina
`>>>
`>>> On May 26, 2008, at 12:56 PM, Kael Fischer wrote:
`>>>
`>>>>I'll try 3) below ... but sometimes that doesn't work ... Look for
`>>>> that email (from transfer big files)
`>>>>
`>>>> On Mon, May 26, 2008 at 12:46 PM, Kael Fischer
`>>>> <kael@derisilab.ucsf.edu>
`>>>> wrote:
`>>>>>
`>>>>> 1) you could give me a place to up load them to or
`>>>>> 2) you could try substituting those *.gz file names, one at a
`>>>>> time, into the urls below and d/l'ing them with a web client (wget
`>>>>> may be more robust than your favorite interactive browser) or
`>>>>> 3) I could upload them to some place like TransferBigFiles.com
`>>>>>
`>>>>> On Mon, May 26, 2008 at 11:49 AM, Christina H. Fan
`>>>>> <chfan@stanford.edu>
`>>>>> wrote:
`>>>>>>
`>>>>>> Hi Kael,
`>>>>>> It would be great if I can get the files over the internet.
`
`STANFORD EXHIBIT 2126
`SEQUENOM v. STANFORD
`CASE IPR2013-00390
`
`
`Sent:
`To:
`Subject:
`
`kael.fischer@gmail.com on behalf of Kael Fischer [kael@derisilab.ucsf.edu]
`Monday, May 26, 2008 2:52PM
`Christina Fan
`Re: GERALD run completed in 08051 O_HWI-EAS1 00_0004_FC20f5baaxx/Data/C1-25
`_Firecrest1.8.28_20-05-2008_kaei!Bustard1.8.28_20-05-2008_kaei/GERALD_20-05-2008
`_kael
`
`Good guess on the match codes. the number in the code it the number of apparent snps. The
`numbers are positions in the reference, and optionally a snp position.
`
`see: http://meebo2.ucsf.edu/Solexa/docs/Whole%20genome%20alignments%20using%20ELAND.html
`
`for more detail
`
`On Mon, May 26, 2008 at 2:10 PM, Christina Fan <chfan@stanford.edu> wrote:
`> hi kael,
`> i am guessing that U stands for unique, NM stands for no match and R
`> stands for repeat. But what is the difference between UO and U1 etc.?
`> And what do the 3 numerical entries in field 4, 5, 6 correspond to?
`> thanks!!!
`> christina
`>
`>
`> On May 26, 2008, at 1:46 PM, Kael Fischer wrote:
`>
`>> I wouldn't count on the transfer big files working.
`>>
`>> use gzip -t after your transfer to test the files.
`>>
`>> kael
`>>
`>> On Mon, May 26, 2008 at 1:03 PM, Christina Fan <chfan@stanford.edu> wrote:
`>>>
`>>> hi kael,
`>>> i managed to download lane1 file with my browser.
`>>> if it's too much of a trouble to do the transferbigfiles i can
`>>>download the file one by one with my browser .. doesn't take too
`>>> long ..
`>>> thanks a lot for your help!
`>>> christina
`>>>
`>>> On May 26, 2008, at 12:56 PM, Kael Fischer wrote:
`>>>
`>>>>I'll try 3) below ... but sometimes that doesn't work ... Look for
`>>>> that email (from transfer big files)
`>>>>
`>>>> On Mon, May 26, 2008 at 12:46 PM, Kael Fischer
`>>>> <kael@derisilab.ucsf.edu>
`>>>> wrote:
`>>>>>
`>>>>> 1) you could give me a place to up load them to or
`>>>>> 2) you could try substituting those *.gz file names, one at a
`>>>>> time, into the urls below and d/l'ing them with a web client (wget
`>>>>> may be more robust than your favorite interactive browser) or
`>>>>> 3) I could upload them to some place like TransferBigFiles.com
`>>>>>
`>>>>> On Mon, May 26, 2008 at 11:49 AM, Christina H. Fan
`>>>>> <chfan@stanford.edu>
`>>>>> wrote:
`>>>>>>
`>>>>>> Hi Kael,
`>>>>>> It would be great if I can get the files over the internet.
`
`STANFORD EXHIBIT 2126
`SEQUENOM v. STANFORD
`CASE IPR2013-00390
`
`
`
`compressed sizes in MB:
`s 1 eland result.txt.gz
`s-2-eland-result.txt.gz
`s-3-eland-result.txt.gz
`s-4-eland-result.txt.gz
`s-6-eland-result.txt.gz
`s-7-eland-result.txt.gz
`s-8-eland=result.txt.gz
`
`>>>>>> Can I download them somewhere somehow?
`>>>>>>Thanks!
`>>>>>> Christina
`>>>>>>
`>>>>>>
`>>>>>>
`>>>>>> Quoting Kael Fischer <kael@derisilab.ucsf.edu>:
`>>>>>>
`>>>>>>> FYI -
`>>>>>>>
`>>>>>>> Here are links to the gerald output.
`>>>>>>>
`If all
`>>>>>>> I'm not sure you need to come here to get the output.
`>>>>>>> you want are the eland result files, they compress down fairly
`>>>>>>> well.
`>>>>>>>
`>>>>>>> Their
`>>>>>>> 164M
`>>>>>>> 134M
`>>>>>>> 183M
`>>>>>>> 194M
`>>>>>>> 206M
`>>>>>>> 178M
`>>>>>>> 163M
`>>>>>>>
`>>>>>>>
`>>>>>>> we could send those over the internets somehow.
`>>>>>>>
`>>>>>>> Kael
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>> ---------- Forwarded message ---------(cid:173)
`>>>>>>> From: <SecondLife-18@ucsf.edu>
`>>>>>>> Date: Sat, May 24, 2008 at 11:43 PM
`>>>>>>> Subject: GERALD run completed in
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>> 080510 HWI-EAS100 0004 FC20f5baaxx/Data/C1-25 Firecrest1.8.28 20
`>>>>>>> -05-2008 kael/Bustard1~8.28 20-05-2008 kael/GERALD 20-05-2008-ka
`>>>>>>> el
`>>>>>>> To: Gerald Reports <kael@derisilab.ucsf.edu>
`>>>>>>>
`>>>>>>>
`>>>>>>> Report sent from SecondLife-18 via derisilab.ucsf.edu port 25 at
`>>>>>>> Sat May 24 23:43:51 2008
`>>>>>>>
`>>>>>>> Links to output files:
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>> http://meebo2.ucsf.edu:4122/Solexa/Run Folders/080510 HWI-EAS100
`>>>>>>>
`0004 FC20f5baaxx/Data/C1-25 Firecrestl.8.28 20-05-2008 kael/Bus
`>>>>>>> tard1~8.28 20-05-2008 kael/GERALD 20-05-2008-kael/Error~htm
`-
`-
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>> http://meebo2.ucsf.edu:4122/Solexa/Run Folders/080510 HWI-EAS100
`>>>>>>>
`0004 FC20f5baaxx/Data/C1-25 Firecrestl.8.28 20-05-2008 kael/Bus
`>>>>>>> tard1~8.28 20-05-2008 kael/GERALD 20-05-2008-kael/IVC.htm
`-
`-
`>>>>>>>
`>>>>>>>
`
`
`
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>> http://meebo2.ucsf.edu:4122/Solexa/Run Folders/080510 HWI-EAS100
`>>>>>>>
`0004 FC20f5baaxx/Data/C1-25 Firecrestl.8.28 20-05-2008 kael/Bus
`>>>>>>> tard1~8.28 20-05-2008 kael/GERALD 20-05-2008-kael/All.htm
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>> http://meebo2.ucsf.edu:4122/Solexa/Run Folders/080510 HWI-EAS100
`>>>>>>>
`0004 FC20f5baaxx/Data/C1-25 Firecrestl.8.28 20-05-2008 kael/Bus
`>>>>>>> tard1~8.28 20-05-2008 kael/GERALD 20-05-2008-kael/Perfect.htm
`-
`-
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>> http://meebo2.ucsf.edu:4122/Solexa/Run Folders/080510 HWI-EAS100
`>>>>>>>
`0004 FC20f5baaxx/Data/Cl-25 Firecrestl.8.28 20-05-2008 kael/Bus
`>>>>>>> tard1~8.28 20-05-2008 kael/GERALD 20-05-2008-kael/Hist.htm
`-
`-
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>> http://meebo2.ucsf.edu:4122/Solexa/Run Folders/080510 HWI-EAS100
`>>>>>>>
`0004 FC20f5baaxx/Data/C1-25 Firecrestl.8.28 20-05-2008 kael/Bus
`>>>>>>> tard1~8.28 20-05-2008 kael/GERALD 20-05-2008-kael/Info.htm
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>> http://meebo2.ucsf.edu:4122/Solexa/Run Folders/080510 HWI-EAS100
`>>>>>>>
`0004 FC20f5baaxx/Data/C1-25 Firecrestl.8.28 20-05-2008 kael/Bus
`>>>>>>> tard1~8.28_20-05-2008 kael/GERALD_20-05-2008-kael/Surnmary.htm
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>>
`>>>>>>> Kael Fischer, Ph.D
`>>>>>>> DeRisi Lab - Univ. Of California San Francisco 415-514-4320
`>>>>>>>
`>>>>>>
`>>>>>>
`>>>>>>
`>>>>>
`>>>>>
`>>>>>
`>>>>>
`>>>>> Kael Fischer, Ph.D
`>>>>> DeRisi Lab - Univ. Of California San Francisco 415-514-4320
`>>>>>
`>>>>
`>>>>
`>>>>
`>>>>
`>>>> Kael Fischer, Ph.D
`>>>> DeRisi Lab - Univ. Of California San Francisco 415-514-4320
`>>>
`>>>
`>>
`>>
`
`
`
`>>
`>>
`>> Kael Fischer, Ph.D
`>> DeRisi Lab - Univ. Of California San Francisco 415-514-4320
`>
`>
`
`Kael Fischer, Ph.D
`DeRisi Lab - Univ. Of California San Francisco 415-514-4320
`
`
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